Passenger service was mostly eliminated by the 1961 merger, but several trains remained for a few more years. These were a Saint Paul to Duluth daytime train known only as Trains 62 and 63 (discontinued June 1961);[4] the overnight Chicago to Duluth Laker and its Saint Paul connection (both discontinued January 15, 1965);[5] the Twin Cities to WinnipegWinnipeger (discontinued March 25, 1967);[5] and the Saint Paul to Portal, North DakotaSoo-Dominion that during the summer, ran through to Vancouver via a connection with Canadian Pacific Railway's The Dominion at Moose Jaw. It was discontinued in December 1963,[6] and the western Canada cars were handled on the Winnipeger for two more summers before they too were pulled. The Soo Line's last passenger train was the Copper Country Limited, a joint service with the Milwaukee Road inherited from the Duluth, South Shore and Atlantic. This Chicago-Champion-Calumet service was discontinued May 8, 1968.[5] In addition there were several mixed trains, with additional ones created to enable the discontinuance of the Saint Paul to Portal passenger train. Some mixed train services gained notoriety because passengers were conveyed in one direction only.

Soo Line boxcar, seen in 2010.

In 1984, CP incorporated the Soo Line Corporation in Minnesota as a holding company, exchanging stock in December to give the Soo Line Corporation total control over the railroad. Two months later, on February 19, 1985, the Soo Line purchased the property of the bankruptChicago, Milwaukee, St. Paul and Pacific Railroad and assigned it to a newly created subsidiary, The Milwaukee Road, Inc. This company and the MN&S were both merged into the Soo Line Railroad effective January 1, 1986. To cut costs, the Soo Line created the Lake States Transportation Division (LSTD) on February 10, 1986[7] to operate the less-important lines, including the ex-Wisconsin Central line between Chicago and the Twin Cities. Unable to implement its proposed labor rule changes, the Soo Line sold the approximately 2,000-mile (3,200 km) LSTD to a new regional railroad, Wisconsin Central Ltd., in 1987 for $133 million.[8] In 1990, CP gained full control of the Soo Line Corporation, of which it had previously owned about 56% of the common stock.[3] In the 2000s, the Soo line was consolidated into CP. Only few Soo locomotives remain in the old paint scheme. Most have been repainted into CP or scrapped.

The Soo Line Trail was created from former pieces of the railroad which has extended down into the Lake Wobegon Trail. The trails are enjoyed by walkers, runners, and bikers in the area and prized for how flat they are.